[med-svn] [bowtie2] branch upstream updated (cce9c2f -> 7b7c16b)
Andreas Tille
tille at debian.org
Mon Jan 9 12:30:48 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository bowtie2.
from cce9c2f Imported Upstream version 2.2.9
new 7b7c16b New upstream version 2.3.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 26 +
.travis.yml | 20 +
MANUAL | 25 +-
MANUAL.markdown | 26 +-
Makefile | 87 +-
NEWS | 23 +-
README | 8 +
VERSION | 2 +-
aligner_result.cpp | 2 +-
aligner_result.h | 2 +-
aligner_seed.cpp | 16 +-
aligner_seed2.cpp | 19 +-
aligner_seed2.h | 2 -
aligner_sw_common.h | 13 +-
aligner_swsse_ee_i16.cpp | 1 -
aligner_swsse_ee_u8.cpp | 1 -
aligner_swsse_loc_u8.cpp | 1 -
aln_sink.h | 8 -
alphabet.cpp | 199 -
alphabet.h | 72 -
bt2_build.cpp | 14 +-
bt2_inspect.cpp | 6 +-
bt2_search.cpp | 207 +-
cpu_numa_info.cpp | 9 +
cpu_numa_info.h | 6 +
diff_sample.h | 2 +-
doc/images/bowtie_logo.png | Bin 0 -> 16419 bytes
doc/images/osi-certified.gif | Bin 0 -> 2712 bytes
doc/images/sflogo.png | Bin 0 -> 1177 bytes
doc/images/university.small.horizontal.white.png | Bin 0 -> 35224 bytes
doc/manual.html | 1417 +++---
doc/release.txt | 153 +
doc/website/faq.shtml | 34 +
doc/website/faq.ssi | 68 +
doc/website/foot.ssi | 12 +
doc/website/index.html | 9 +
doc/website/index.shtml | 60 +
doc/website/manual.shtml | 33 +
doc/{manual.html => website/manual.ssi} | 36 +-
doc/website/news.shtml | 35 +
doc/website/old_news.ssi | 359 ++
doc/website/other_tools.shtml | 33 +
doc/website/push.sh | 17 +
doc/website/push_images.sh | 16 +
doc/website/recent_news.ssi | 104 +
doc/website/rhsidebar.ssi | 196 +
doc/website/top.ssi | 16 +
dp_framer.cpp | 3 +-
dp_framer.h | 3 +-
filebuf.h | 1 +
opts.h | 2 +-
pat.cpp | 2030 ++++-----
pat.h | 1852 +++-----
pthreadGC2.dll | Bin 0 -> 60273 bytes
read.h | 102 +-
read_qseq.cpp | 383 +-
ref_read.cpp | 34 +-
sam.cpp | 120 +-
sam.h | 8 -
scoring.cpp | 1 -
scoring.h | 2 +-
scripts/sa.py | 79 +
scripts/sim/AlignmentCheck.pm | 859 ++++
scripts/sim/DNA.pm | 287 ++
scripts/sim/Mutate.pm | 301 ++
scripts/sim/RandDNA.pm | 191 +
scripts/sim/SampleRead.pm | 244 ++
scripts/sim/Sim.pm | 1040 +++++
scripts/sim/Test.pm | 47 +
scripts/sim/contrib/ForkManager.pm | 412 ++
scripts/sim/run.pl | 133 +
scripts/sim/run.sh | 37 +
scripts/sim/unit.sh | 23 +
scripts/test/.gitignore | 1 +
scripts/test/DNA.pm | 127 +
scripts/test/README.md | 44 +
scripts/test/benchmark/benchmarks.py | 275 ++
scripts/test/benchmark/data/conf/acc.json | 44 +
scripts/test/benchmark/data/conf/seta.bench | 59 +
scripts/test/benchmark/data/conf/speed.json | 44 +
scripts/test/benchmark/run.py | 128 +
scripts/test/benchmark/samreader.py | 128 +
scripts/test/big_data/reads/human_reads.fa | 8 +
scripts/test/big_data/reads/mouse_reads.fa | 8 +
scripts/test/bt2face.py | 39 +
scripts/test/btdata.py | 199 +
scripts/test/dataface.py | 81 +
scripts/test/large_idx.py | 110 +
scripts/test/regressions.py | 207 +
scripts/test/simple_tests.pl | 5070 ++++++++++++++++++++++
scripts/test/simple_tests.sh | 34 +
search_globals.h | 5 -
simple_func.h | 4 +
sstring.cpp | 4 +-
sstring.h | 142 +-
threading.h | 46 +-
96 files changed, 14429 insertions(+), 3967 deletions(-)
create mode 100644 .gitignore
create mode 100644 .travis.yml
create mode 100644 README
create mode 100644 cpu_numa_info.cpp
create mode 100644 cpu_numa_info.h
create mode 100644 doc/images/bowtie_logo.png
create mode 100644 doc/images/osi-certified.gif
create mode 100644 doc/images/sflogo.png
create mode 100644 doc/images/university.small.horizontal.white.png
create mode 100644 doc/release.txt
create mode 100644 doc/website/faq.shtml
create mode 100644 doc/website/faq.ssi
create mode 100644 doc/website/foot.ssi
create mode 100644 doc/website/index.html
create mode 100644 doc/website/index.shtml
create mode 100644 doc/website/manual.shtml
copy doc/{manual.html => website/manual.ssi} (97%)
create mode 100644 doc/website/news.shtml
create mode 100644 doc/website/old_news.ssi
create mode 100644 doc/website/other_tools.shtml
create mode 100644 doc/website/push.sh
create mode 100644 doc/website/push_images.sh
create mode 100644 doc/website/recent_news.ssi
create mode 100644 doc/website/rhsidebar.ssi
create mode 100644 doc/website/top.ssi
create mode 100644 pthreadGC2.dll
create mode 100644 scripts/sa.py
create mode 100644 scripts/sim/AlignmentCheck.pm
create mode 100644 scripts/sim/DNA.pm
create mode 100644 scripts/sim/Mutate.pm
create mode 100644 scripts/sim/RandDNA.pm
create mode 100644 scripts/sim/SampleRead.pm
create mode 100644 scripts/sim/Sim.pm
create mode 100644 scripts/sim/Test.pm
create mode 100644 scripts/sim/contrib/ForkManager.pm
create mode 100644 scripts/sim/run.pl
create mode 100644 scripts/sim/run.sh
create mode 100644 scripts/sim/unit.sh
create mode 100644 scripts/test/.gitignore
create mode 100644 scripts/test/DNA.pm
create mode 100644 scripts/test/README.md
create mode 100755 scripts/test/benchmark/benchmarks.py
create mode 100644 scripts/test/benchmark/data/conf/acc.json
create mode 100644 scripts/test/benchmark/data/conf/seta.bench
create mode 100644 scripts/test/benchmark/data/conf/speed.json
create mode 100755 scripts/test/benchmark/run.py
create mode 100755 scripts/test/benchmark/samreader.py
create mode 100644 scripts/test/big_data/reads/human_reads.fa
create mode 100644 scripts/test/big_data/reads/mouse_reads.fa
create mode 100755 scripts/test/bt2face.py
create mode 100755 scripts/test/btdata.py
create mode 100755 scripts/test/dataface.py
create mode 100755 scripts/test/large_idx.py
create mode 100755 scripts/test/regressions.py
create mode 100644 scripts/test/simple_tests.pl
create mode 100644 scripts/test/simple_tests.sh
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